Spiny dogfish, grad school, and life

My Thesis: The Liner Notes

May 9, 2012

Whew. What a semester end that was (I’m still trying to survive the fallout). The first year of the PhD is down, and with it hopefully most of my class load so I can get to the fun stuff. This year also saw the official finishing of my Master’s thesis, which due to the vagaries of due dates has only shown up online recently (and I’m still waiting on the bound copies…). For those who haven’t checked it out yet, you can find the full text in glorious, open-access pdf format here, complete with only a few formatting errors. Feel free to peruse it, use parts of it (with proper citation of course), and contact me with any critiques or advice. The citation format (in AFS format at least) for it would be:

Bangley, C. W. 2012. Food and feeding habits of the spiny dogfish Squalus acanthias overwintering off the coast of North Carolina and the effects on the marine community. Master’s Thesis. East Carolina University, Greenville, NC.

Rather than summarize all the findings and dive into the nitty-gritty of the procedures (which you can get by actually reading the document), I’ll be giving the “behind the thesis” tour of this big paper I spent two and a half years writing. With any luck, it’ll be somewhat entertaining. It will also serve as a sort of retrospective before I start ramping up the blog to cover my dissertation work this summer.

The NOAA R/V Henry B. Bigelow, my home for over three weeks in March 2010.

Introduction – The dirty little secret of this introduction is that it’s about 90 % the same paper I wrote up as my thesis proposal. I finished writing it in early 2010 and defended it about a week before heading up to my old stomping grounds of Rhode Island to catch the NOAA R/V Henry B. Bigelow. The drive from Greenville, NC to Newport, RI is 12 hours with perfect traffic and leeway for speeding, and it was after 9 p.m. by the time I got up there. Unfortunately, the Bigelow was docked at the Newport naval base and I would need to clearance to get aboard. The office I’d need to go through was closed until the next morning, and my name wasn’t on the list left with the gate guard. After some tense moments during which I was afraid I was about to get shot or hauled off by the Military Police before I could even set foot on the boat, I was told to come back in the morning. Fortunately, I still have some friends in Newport and was able to secure a couch for the night.

The details of the cruise, where I got about half of my data (the other half graciously collected by Dr. Rulifson and Coley Hughes aboard the R/V Cape Hatteras), can be found in the series of posts beginning with this one. In short, I spent an entire day more seasick than I’ve ever been, saw marine life I’d only dreamed of seeing as a kid, made over 160 dogfish vomit up their latest meals, and grew the most disappointing field work beard ever (though my beard-growing speed has increased rapidly since then. Maybe this trip let my facial hair know it’s okay to occasionally grow out). Definitely a great experience.

In the end, some of the proposed methods outlined in the Introduction worked out, while others proved way too ambitious. Not bad for a project that only squeaked approval in just before jumping aboard the boat.

I sympathized with this dogfish both during my seasickness and while trying to get this chapter published.

Chapter 1: Nonlethal Puking – One of my goals for this thesis work was to experiment with a nonlethal technique of collecting stomach contents from dogfish-sized sharks. This particular technique, called “stomach tube lavage,” involves shoving a tube down the shark’s throat, flushing it with water, and letting everything tumble out. Highly unpleasant for the shark, but it has to beat getting killed and cut open right?

Dogfish are an ideal subject for this sort of thing because a.) they’re numerous enough to be readily available, b.) they’re almost ridiculously hardy, and c.) they’ve been used as a “model” shark for testing different sampling and lab methods that can then be adapted to other species. Overall, I felt pretty good about myself for trying it out, figuring that even if the only successful publication I’d get out of this thesis was how to nonlethally sample stomach contents, then at least I’d save a few sharks. So in a prime example of “breaking eggs to make an omelet,” I humanely sacrificed some of the tubed sharks to see how much food was successfully removed.

This chapter went over well at my thesis defense, but upon trying to get it published it became clear that there were a couple glaring errors that ensured that no, this chapter would never be published on its own. The efficiency was good but not great during sampling, but I hypothesized that the larger dogfish needed one more tube size up to retrieve the optimum amount of puke. The reviewers read this in the first draft and said, “okay, go try the next tube size up.” I got some extra lavages in while helping out with field work off of Cape Cod, and using the next tube size up found that it was very possible to get the entire contents of the stomach out using tube lavage. “Awesome,” I thought, and sent out a revision. The reviewers then asked if I’d recorded the number of flushes and the individual handling time for each shark, things that any rational thinking human being should be recording for this kind of paper. Well, I blew that part. I tried to write my way around it by estimating the individual handling time using the time between tows on the Bigelow and dividing it by the number of sharks lavaged, but the reviewers saw through my b.s. and rightfully rejected the paper. Peer review works.

One of the reviewers made a comment after the first draft that the results of this chapter would be best served by folding them into a larger paper on the rest of the thesis. Turns out if I’d listened to reviewer #3 in the first place, I’d have saved myself almost a year of bouncing revisions back and forth. So that’s the strategy I’ll be taking to get my lavage efficiency estimates out. I bear the reviewers and journal no ill will and hope to submit something more deserving to them in the future. In the meantime, I’m still pretty proud of how well I got this method to work, so feel free to cite the thesis if you need an example of nonlethal methods, and know that it’s the product of lot of hard work, if not quite enough data to make its own paper.

Chapter 2: Boys and Girls – This thesis quickly became a tale of two data sets. The data collected aboard the Cape Hatteras was comprised almost entirely of large adult dogfish, which tend to have the most impressive stomach contents, but I wanted to try and break the sharks down into demographics to see if there were any shifts in diet with size or sex. This chapter used data from the Bigelow only, since that cruise covered a variety of depths and shark sizes. Unfortunately, there weren’t as many dogfish sampled in this survey so I had to really stretch to make some of the connections. Ultimately, I had a lot of cool results in this chapter from some unfortunately-sized sample sizes. As cool as it was that I was able to tentatively identify the size range at which my dogfish switched from krill to fish, there just weren’t many samples on the smaller side of that cut-off.

Breaking the diet up by sex was a lot more conclusive, and produced some nice pieces of data that I hope to get out somewhere. The sex-diet-habitat connection I was able to make is, as far as I’ve been able to tell, the first time anyone’s tried to make that connection for dogfish. The results impressed one of my labmates enough that he’s planning to cite my thesis in a paper he wants to get published. If someone else gets published referencing my unpublished data, that makes me a published author, right? Maybe my thesis will become a citation classic.

One of my favorite examples of dogfish-inflicted carnage. Photo by Ben Bangley.

Chapter 3: Nom Nom Nom – This chapter was really the point of the entire thesis, which was to document and try to quantify just how many of our favorite fish end up in the jaws of spiny dogfish. The Bigelow data proved to be hodgepodge of whatever was available as prey, but the Cape Hatteras data suggested something rather interesting going on with dogfish feeding in February. Atlantic menhaden (the most important fish in sea due to being eaten by just about everything) dominated the dogfish diet in the Cape Hatteras samples. This may be important because menhaden have been in decline due to overfishing and habitat degradation, so there is a lot of interest among fisheries managers in finding out what the level of natural mortality is for these fish. Again, everything eats them, so that’s tough to quantify, but I was at least able to get a decent estimate for the dogfish part of the equation. Also interesting, dogfish apparently use their impressive teeth to chop up not just large fish being scavenged out of nets, but also large fish that they’re actively pursuing. Maybe there is something to dogfish being part piranha…

One stumbling block for finding out how much dogfish eat is that the current estimate for spiny dogfish daily ration is based on the population in the North Pacific, which in 2010 was recognized as a separate species and has always been noted for being larger and slower growing than our Atlantic dogfish. This has created a need for someone to figure out how fast Atlantic dogfish digest their prey, which in turn tells us how much food they need and how much fish they can eat. Don’t worry guys, I’m on it. More info on that in my next post.

Chapter 4: Two Predators – In North Carolina fisheries management, very few people get by without having to deal with striped bass. Sometimes it’s tough to tell that there are any other fish in the sea at all. I had hoped to find evidence of predation on some larger fish while I was going through my shark puke, but imagine my glee when, of all fish, stripers started showing up in dismembered chunks. Granted I didn’t find many, but I’m not the only person to find stripers in the bellies of these ferocious little sharks: they show up in dogfish guts in both the NEAMAP and ChesMMAP surveys, and you can look up the data yourself on VIMS’ website if you don’t believe me.

Using the same technique from Chapter 3, I estimated the quite low level of predation on striped bass. I wanted to explore this relationship further because, as largeish fish-eating predators, these two species are very evenly-matched ecologically. I looked at dietary and spatial overlap, and even delved into a little predator/prey interaction theory in attempting to explain how dogs and stripers might get along in the wild. Interestingly, menhaden are a very important shared prey item, suggesting that the stability of dogfish/striped bass interactions might depend on a readily available supply of those tasty little fish.

Writing this chapter was a blast and I’m looking at tweaking it, adding some more data, and publishing it (I’ve also been speaking about it at ECU, Tidewater, and later this summer at the AES meeting in Vancouver). This chapter also got me really into predator/prey theory, which is a research interest I’d like to stick with (and has definitely influenced the content of this blog).

The Future – So that wraps up my Master’s thesis retrospective. My dissertation work will likely be taking me beyond spiny dogfish, but I’m sure they will play a big role (along with their smooth cousins). I also have a dogfish-specific project or two coming down the pipeline. My next post will detail some of the projects I’ll be working on in the next year. Expect the blog to take on a bit more of a “project log” format this summer, though there will definitely still be room for profiles of other people’s research and fishery management issues. It’s been a wild ride for the first part of my grad school experience. Thanks for reading and commenting, and remember to never underestimate the little guys.